Contacts of the helix formed by residues 657 - 672 (chain G) in PDB entry 2VKZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 657 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625G PHE* 3.2 36.8 - + + -
626G SER* 5.4 0.9 - - - -
655G ASN* 3.0 11.0 + - - +
656G PRO* 1.3 78.8 - - + +
658G MET* 1.3 68.5 + - + +
660G GLN* 2.9 37.0 + - - +
661G TRP* 3.2 28.6 - + + -
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Residues in contact with MET 658 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621G GLY* 3.6 32.5 - - - +
622G GLY* 4.6 2.9 - - - +
624G TYR 4.9 2.7 - - - +
625G PHE* 6.5 0.2 - - + -
651G LEU* 3.7 22.9 - - + -
652G ILE* 2.8 59.7 - - + +
655G ASN* 2.8 29.0 + - + +
657G PHE* 1.3 75.2 - - + +
659G LEU* 1.3 54.2 + - - +
660G GLN 2.9 0.5 + - - -
661G TRP* 3.2 29.3 + - + +
662G GLY* 2.8 33.8 + - - -
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Residues in contact with LEU 659 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651G LEU* 3.9 23.1 - - + -
652G ILE 3.6 16.6 - - - +
653G TYR* 3.1 47.6 - - + +
655G ASN 3.1 13.0 + - - +
656G PRO* 3.8 10.3 - - + +
658G MET* 1.3 76.7 - - - +
660G GLN* 1.3 59.8 + - - +
662G GLY 4.0 1.1 - - - -
663G ILE* 3.1 49.3 + - + +
664G PRO* 4.3 0.3 - - - +
681G ILE* 4.9 5.6 - - + -
694G TYR* 3.6 12.8 - - + +
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Residues in contact with GLN 660 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656G PRO 3.2 14.6 + - - +
657G PHE* 2.9 33.0 + - - +
659G LEU* 1.3 79.1 - - - +
661G TRP* 1.3 61.2 + - - +
662G GLY 3.4 0.2 - - - -
664G PRO* 3.2 22.3 - - - +
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Residues in contact with TRP 661 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621G GLY 5.1 0.9 - - - -
624G TYR* 3.3 42.8 - - + -
625G PHE* 3.3 15.7 + - - +
626G SER* 3.6 15.7 - - - -
627G ALA* 3.3 33.8 - - + +
630G MET* 3.9 24.9 - - + -
651G LEU* 5.4 1.3 - - + -
657G PHE* 3.2 46.6 + + + -
658G MET* 3.2 32.8 - - + +
660G GLN* 1.3 80.1 - - - +
662G GLY* 1.3 69.0 + - - +
664G PRO* 3.9 5.3 - - - +
665G LEU* 3.2 30.8 + - + +
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Residues in contact with GLY 662 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630G MET* 6.2 0.7 - - - -
651G LEU* 4.2 16.2 - - - -
658G MET 2.8 18.3 + - - -
661G TRP* 1.3 92.3 - - - +
663G ILE* 1.3 56.2 + - - +
665G LEU* 2.8 4.9 + - - +
666G ILE* 2.7 36.4 + - - +
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Residues in contact with ILE 663 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651G LEU* 3.6 21.5 - - + +
659G LEU* 3.1 24.8 + - + +
662G GLY* 1.3 73.4 - - - +
664G PRO* 1.3 67.4 - - + +
666G ILE* 3.3 4.2 + - + +
667G LYS* 3.0 23.3 + - + +
679G LEU* 4.0 12.8 - - + -
681G ILE* 5.1 0.7 - - + -
693G GLU* 4.6 13.7 - - + +
694G TYR* 3.1 47.3 - - + +
697G THR* 6.0 0.7 - - + -
698G LEU* 3.2 28.7 - - + +
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Residues in contact with PRO 664 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659G LEU 4.3 0.4 - - - +
660G GLN 3.2 26.0 - - - +
661G TRP* 3.9 5.8 - - - +
662G GLY 3.6 0.7 - - - -
663G ILE* 1.3 95.6 - - + +
665G LEU* 1.3 57.2 + - - +
667G LYS* 2.9 8.4 + - + +
668G GLU* 2.7 37.3 + - - +
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Residues in contact with LEU 665 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627G ALA* 3.8 23.8 - - + +
630G MET* 3.9 30.3 - - + -
631G THR* 3.2 25.8 - - - +
634G ILE* 4.1 3.8 - - + -
649G ILE* 5.6 0.9 - - + -
661G TRP* 3.2 19.0 + - + +
662G GLY* 2.8 10.9 + - - +
664G PRO* 1.3 75.3 - - - +
666G ILE* 1.3 60.0 + - + +
668G GLU* 3.9 10.5 - - + -
669G LEU* 3.0 63.4 + - + +
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Residues in contact with ILE 666 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649G ILE* 4.3 19.1 - - + -
651G LEU* 3.9 16.4 - - + -
662G GLY 2.7 15.1 + - - +
663G ILE* 3.3 9.4 - - - +
665G LEU* 1.3 75.8 - - + +
667G LYS* 1.3 59.7 + - - +
669G LEU* 3.1 6.2 + - - +
670G ARG* 2.8 30.0 + - + +
676G ILE* 3.9 21.7 - - + +
679G LEU* 3.5 38.8 - - + -
698G LEU* 3.7 25.8 - - + -
700G LEU* 4.4 15.9 - - + -
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Residues in contact with LYS 667 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663G ILE* 3.0 7.8 + - + +
664G PRO* 2.9 11.2 + - + +
666G ILE* 1.3 76.5 - - - +
668G GLU* 1.3 65.0 + - - +
670G ARG* 3.3 6.3 + - - +
671G SER* 3.0 24.9 + - - -
697G THR* 3.2 43.8 - - + +
698G LEU* 3.6 21.3 - - + +
699G GLY 5.7 0.2 - - - +
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Residues in contact with GLU 668 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664G PRO 2.7 21.9 + - - +
665G LEU* 4.0 9.6 - - + +
667G LYS* 1.3 75.4 - - - +
669G LEU* 1.3 67.6 + - + +
671G SER* 2.8 27.0 + - - -
672G LYS* 3.3 35.2 + - - +
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Residues in contact with LEU 669 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631G THR* 4.5 9.6 - - + +
634G ILE* 3.5 41.5 - - + -
665G LEU* 3.0 43.6 + - + +
666G ILE* 3.4 6.7 - - - +
667G LYS 3.0 0.2 - - - -
668G GLU* 1.3 83.7 - - + +
670G ARG* 1.3 64.5 + - - +
672G LYS* 3.0 18.5 + - + +
674G TYR* 3.1 56.7 + - + -
676G ILE* 4.7 4.9 - - + -
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Residues in contact with ARG 670 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666G ILE* 2.8 21.4 + - + +
667G LYS* 3.3 5.1 + - - +
669G LEU* 1.3 76.0 - - - +
671G SER* 1.3 55.2 + - - +
673G GLY* 2.7 37.8 + - - -
674G TYR* 2.9 29.0 + - - +
676G ILE* 3.1 25.0 + - + +
677G GLN* 3.5 18.6 - - - +
699G GLY* 2.7 56.1 + - - +
700G LEU* 3.7 15.7 - - + -
1158G PHE* 4.6 10.7 - - - -
1165G PHE* 4.0 18.6 + - - +
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Residues in contact with SER 671 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667G LYS* 3.0 17.5 + - - -
668G GLU* 2.8 28.3 + - - -
670G ARG* 1.3 76.6 - - - +
672G LYS* 1.3 62.3 + - - +
673G GLY* 3.2 0.7 + - - -
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Residues in contact with LYS 672 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668G GLU* 3.3 36.5 + - - +
669G LEU* 3.0 16.7 + - + +
671G SER* 1.3 83.6 + - - +
673G GLY* 1.3 57.6 + - - +
674G TYR* 3.9 20.6 - - + +
1164G MET* 3.2 17.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il